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Evolutionary Relationships of Ljungan Virus Variants Circulating in Multi-Host Systems across Europe.

Chiara Rossi1 Nicola Zadra1 Cristina Fevola1,2 Frauke Ecke3 Birger Hörnfeldt3 René Kallies4 Maria Kazimirova5 Magnus Magnusson3 Gert E Olsson3,6 Rainer G Ulrich7 Anne J Jääskeläinen8 Heikki Henttonen9 Heidi C Hauffe1
Affiliations 9 institutions
  1. Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all'Adige, TN, Italy.
  2. Department of Virology, Faculty of Medicine, University of Helsinki, FI-00029 Helsinki, Finland.
  3. Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.
  4. Department of Environmental Microbiology Working Group Microbial Interaction Ecology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany.
  5. Slovak Academy of Sciences (SAS), Institute of Zoology, 845 06 Bratislava, Slovakia.
  6. Unit for Nature Conservation, County Administrative Board of Halland County, 301 86 Halmstad, Sweden.
  7. Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany.
  8. HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, FI-00029 Helsinki, Finland.
  9. Wildlife Ecology, Natural Resources Institute Finland (LUKE), FI-00790 Helsinki, Finland.
PMID 34372523 2021 Viruses eng epublish
PubMed DOI Browse context

Article

Publication summary

The picornavirus named 'Ljungan virus' (LV, species <i>Parechovirus B</i>) has been detected in a dozen small mammal species from across Europe, but detailed information on its genetic diversity and host specificity is lacking. Here, we analyze the evolutionary relationships of LV variants circulating in free-living mammal populations by comparing the phylogenetics of the VP1 region (encoding the capsid protein and associated with LV serotype) and the 3D<sup>pol</sup> region (encoding the RNA polymerase) from 24 LV RNA-positive animals and a fragment of the 5' untranslated region (UTR) sequence (used for defining strains) in sympatric small mammals. We define three new VP1 genotypes: two in bank voles (<i>Myodes glareolus</i>) (genotype 8 from Finland, Sweden, France, and Italy, and genotype 9 from France and Italy) and one in field voles (<i>Microtus arvalis</i>) (genotype 7 from Finland). There are several other indications that LV variants are host-specific, at least in parts of their range. Our results suggest that LV evolution is rapid, ongoing and affected by genetic drift, purifying selection, spillover and host evolutionary history. Although recent studies suggest that LV does not have zoonotic potential, its widespread geographical and host distribution in natural populations of well-characterized small mammals could make it useful as a model for studying RNA virus evolution and transmission.

bank vole Ljungan virus isolates Parechovirus B Picornaviridae rodent-borne virus small mammals zoonosis Evolution, Molecular Host Specificity Phylogeny 5' Untranslated Regions Animals Europe Genetic Variation Genotype Mammals Parechovirus Picornaviridae Infections

Structured evidence records

Evidence records

5 total
Zoonotic Surveillance 3 records
Zoonotic Surveillance Extraction confidence 0.90
Key finding

Ljungan virus RNA was detected in 24 free-living small mammals across Europe, providing genomic surveillance of viral diversity and distribution across host species.

Virus
LV
Host
Mammalia
Location
Europe
Supporting text

Ljungan virus has been detected in a dozen small mammal species from across Europe. We analyze the evolutionary relationships of LV variants circulating in free-living mammal populations by comparing the phylogenetics of the VP1 and 3Dpol regions from 24 LV RNA-positive animals.

Method
phylogenetic analysis; RNA detection
Geographic raw
Europe
Zoonotic Surveillance Extraction confidence 0.90
Key finding

Genomic surveillance identified three new Ljungan virus VP1 genotypes, two in bank voles and one in field voles sampled from several European countries.

Virus
LV
Location
Finland France Sweden Italy
Supporting text

We define three new VP1 genotypes: two in bank voles (Myodes glareolus) (genotype 8 from Finland, Sweden, France, and Italy, and genotype 9 from France and Italy) and one in field voles (Microtus arvalis) (genotype 7 from Finland).

Method
phylogenetic analysis; VP1 genotyping
Geographic raw
Finland, Sweden, France, and Italy
Zoonotic Surveillance Extraction confidence 0.90
Key finding

Surveillance in Finland detected a new Ljungan virus VP1 genotype (genotype 7) in field voles.

Virus
LV
Location
Finland Finland
Supporting text

We define three new VP1 genotypes: ... one in field voles (Microtus arvalis) (genotype 7 from Finland).

Method
phylogenetic analysis; VP1 genotyping
Geographic raw
Finland
Country inferred
Finland
Cross Species Transmission 1 records
Cross Species Transmission Extraction confidence 0.80
Key finding

Ljungan virus is circulating among multiple small mammal species in Europe, supporting animal-to-animal viral transmission within a multi-host system.

Virus
LV
Location
Europe
Supporting text

The picornavirus named 'Ljungan virus' (LV, species Parechovirus B) has been detected in a dozen small mammal species from across Europe, and LV variants circulate in free-living mammal populations in sympatric small mammals.

Method
VP1 region sequencing; 3Dpol region sequencing; phylogenetic analysis
Study design
phylogenetic analysis
Transmission direction
animal-to-animal
Geographic raw
Europe
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.95
Key finding

Phylogenetic analyses of VP1, 3Dpol, and 5' UTR sequences from Ljungan virus isolates in European small mammals revealed three new VP1 genotypes and host-associated viral diversification.

Virus
LV
Host
Mammalia
Location
Not specified
Supporting text

We analyze the evolutionary relationships of LV variants ... by comparing the phylogenetics of the VP1 region ... and the 3Dpol region ... and a fragment of the 5' untranslated region (UTR) sequence ... in sympatric small mammals.

Genes or proteins
VP1; 3Dpol; 5' untranslated region
Analysis methods
phylogenetic analysis; comparative genomic analysis